Abstract Our overall objective in this high-risk high-reward application is to determine the mechanisms underlying enhanced bone formation and density in single nucleotide polymorphisms located in the RUNX1 gene locus. We provide proof of concept evidence indicating that the previously described two regions associated with enhanced bone mineral density, which are located near the RUNX1 gene, have the potential for interactions with this gene and other gene loci. Our proof of feasibility includes our ability to manipulate and target iPSCs, perform unbiased long-range interaction assays using circularized chromatin conformation capture sequencing (4C-Seq) to identify specific interactions between the BMD associated variant regions and target genes. Finally, we show our ability to induce mesenchymal progenitor cell-mediated osteogenesis in vitro and in a model of bone regeneration in vivo. Our hypothesis posits that single nucleotide polymorphisms in the noncoding region near or within RUNX1 identify functional genomic sequences in close association that directly regulate RUNX1 expression through long-range interactions. Thus, we propose to first determine whether regulatory regions harbored in the RUNX1 locus are required for osteogenesis, chondrogenesis and osteoclastogenesis in vitro as well as for bone formation and mineral bone density in vivo (Aim 1). We will also examine whether regulatory elements within the RUNX1 locus influence osteogenic differentiation and mineralization through interaction with other target genes (Aim 2). Our proposed studies will for the first time establish whether GWAS loci associated with changes in bone mineral density are functionally required for chondrogenic and or osteogenic differentiation and maturation. Moreover, we propose to identify the regulatory targets of the BMD-GWAS associations and their potential function in osteoblasts.